TARDIS Adventures
by Skarfly
Summary: The Doctor tries desperately to get back to his own universe; meeting all sorts of faces and leaving his own print on the universes he passes through; meanwhile something darker is at play... [One OC spot open]
1. Chapter 1

Location: UNSC ship

Captain Keyes was flying his ship away from a covenant attack on Reach; the planet's surface had been burned to glass

After the cut scene where the chief got out on an escape pod

"Chief" Cortana warned, "I'm detecting another rift; something else is coming at us."

"What is it?" the Chief asked

"It's… that's not possible…" Cortana sounded surprised, "It's a phone box."

The blue box seared past the UNSC pod and landed on the surface of the ring

[Dun nun nun nun; dun nun nun nun; dun dun nun nun! Dun dun nun nun!]

Skarfly as: The Doctor

[Pending] as: The Companion

(I need a request for the Doctor's companion; send one in quick! One opening!)

The pod landed on a cliff not too far away from the box; Cortana marked it with his HUD

"It landed by the other life boat; I'd suggest you go over there and check it out." Cortana said

The Chief picked up a few weapons and walked there; leaving the empty pod behind

"What's a blue box doing on this ring?" the Chief asked

"I'm not sure; it wasn't covenant and it looked like a normal call box." Cortana answered

The Chief continued; dispatching a few small groups of covenant along the way; until he found the second area where the other escape pod landed

He also saw the blue box; on the outer edge of the area

The marines had the box surrounded; Johnson had walked up to the chief

"Hey there Chief; I thought we were cooked."

"What is that thing?" Cortana asked

"I have no idea sir" Johnson said, "But it came out of space at the same time we did."

*Creak*

"Huh" a voice said; slightly British, "Yet another welcoming like this."

The Chief turned around and saw a man in the doorway of the box, his hair was brown and had a crest; his outfit was a brown coat and a white polo shirt, his pants were dark blue and his shoes were dark brown; his necktie was bright red

"Who are you?" Cortana demanded through the Chief's speakers

"That's easy; I'm the Doctor." The man said

"What's your degree?" A marine asked

"I'm not a doctor in medicine; that's my name." the Doctor said

"How can your name be Doctor?" Cortana asked

"Well-" a plasma shot flew over his head, "Now I know why you had the guns."

"Keep the Doctor covered" Cortana ordered, "He can't answer questions when he's dead."

"Doctor!" Johnson waved, "This way!"

The Doctor checked to see he had what he needed; then he sprinted across the field

Several plasma bolts flew over his head while he made a break for it; once again the air tasted odd; as if the universe was off

"Did I land in the right place?" the Doctor asked as he got into cover

"In a battle zone?" a marine asked, "Not a place for a civilian."

"Who said I was a civilian?" the Doctor asked

"Certainly dressed like one." Cortana chimed in

The Doctor walked over to a dead grunt on the structure; he took out his sonic and scanned it

"I wonder why this is happening." The Doctor said

"Why what is happening?" the marine asked; seemingly not leaving the Doctor unattended

"This whole war; there's bound to be a reason." The Doctor stood up

"I can tell you're not from around here Doctor" the marine said, "But honestly I think you're a bit slow on the update."

"What's your name?"

"I'm Private Jenkins" the marine smiled slightly, "Anyway I think the Chief is done."

The Doctor walked towards the TARDIS; but the Chief got in his way

"What's in the box?" he asked

"Can't say" the Doctor said, "But I'll be fine; you take care of yourself."

The Chief put a heavy hand on the Doctor's shoulder; and the Doctor's smile vanished

"Oh, You really don't want to do that" the Doctor said

"And why not?" the Chief demanded

The Doctor took out the sonic and held it, "I'm giving you one warning; if you try and stop me from getting to the TARDIS your mission will get a lot more difficult."

The Chief didn't let go

"That was your one warning" the Doctor used the sonic on the Chief's helmet

His HUD winked out and his display was fuzzing, the armor sparked and the shields dropped to zero

The Doctor wriggled out of his grasp and ran into the TARDIS; locking the door behind him

"They never listen do they?" the Doctor thought aloud

The Doctor looked at the interior of the TARDIS; the lighting was the same

"Where am I anyway; a giant ring in the middle of space…" the Doctor tried to put pieces together, "There's something I'm missing here…"

The Doctor then walked up to the console and hit a blinking button; it was a transmission

"_Chief; forget the box and get to the objective; there's something in the ring._" A male voice ordered

"This may be worth looking into" the Doctor hit a button and started the TARDIS to arrive several hours later

"Right; I can use the bio signatures from that armored human to land where he'll be now." The Doctor opened the door

* * *

An elite walked onto the bridge of one ship; the holy ship where the high prophets were kept

He kneeled, "I have arrived holy ones."

"Rise commander" a raspy voice said, "We have something to show you."

The elite stood up; marveling at the walls

"I haven't heard of this prophecy." The elite pointed at a carving

"It is one that was obscure Commander" the prophet of Truth said, "It tells that after the ring is found that something else will be discovered."

"A blue box will appear; and hold the key to our victory, or our destruction." The prophet of Mercy finished

"Excuse me holy ones" the elite shifted from foot to foot, "Did you say blue box?"

"Have you seen this blue box?" Truth asked calmly

"Yes; but when the creature stepped out" the elite took a breath, "A human stepped out."

"And so our only hope to kill the humans" Mercy said, "Is a human."

"Capture this human" Truth ordered, "We will not have him assisting the humans."

The Elite nodded and left


	2. An unexpected guest

Chapter 2: An unexpected guest

The Doctor heard something clink; he turned to see a pony standing there; she was a unicorn and her mane was black with blue highlights on the tips; it had a blue sheen to it

Her coat was silver; with the same bluish shine to it

Her eyes were blue and large with surprise

"What!" The Doctor turned around

"Where am I?" the unicorn asked

"What!" The Doctor repeated

"What am I doing here?" the unicorn seemed unsure

"Okay okay" the Doctor calmed down, "Who are you?"

"Starlight" she said, "Now you answer one of my questions."

"This is the TARDIS" the Doctor said, "How did you get in here?"

"You left the door open when you said goodbye back in Equestria." Starlight answered

"And you just trotted in?" the Doctor vented, "I told them this was dangerous enough! Een more so with a stowaway!" he sighed, "What were you thinking?"

"I wanted to see the stars" Starlight said, "Not sit around without a meaning."

The Doctor smiled a bit, "I understand that; but I would have preferred I was told before I left that universe."

"Left the-" Starlight was cut off by the TARDIS jerking to the side

"Where are we going now?" the Doctor checked the console

The TARDIS settled

"Who are you?" Starlight asked

"I'm the Doctor" the Doctor answered

Starlight stiffened, "Why aren't you a pony?"

The Doctor turned to her, "What?"

"The last time I met you. You were a pony then."

The Doctor slapped his palm against his forehead

"Of course! Alternate universe alternate Doctor! But why didn't he approach me back when I was there…?"

The TARDIS made a noise

"Right then" the Doctor clapped his hands together, "Let's see where we landed."

He opened the doors and stepped outside; Starlight followed

They landed in a spot where the walls were metal; the floor and ceiling weren't too far apart; there were strapped dissection tables; littered with bodies

The Doctor gasped; then he ran to the side of one man

His hair was blonde; he was known as Saxon; or as the Master

"What is this place…?" the Doctor thought out loud

"_Hello and welcome to our wonderful factory_" a voice said, "_Please leave the failed subjects alone as they have already left testing._"

"Testing for what?" Starlight asked

"Who are you?" the Doctor demanded, "And why is this place holding dead Timelords?"

"_I see you're a clever one_" the voice was female; amused, "_However you're too clever to remain alive._"

A robotic arm grabbed the Doctor's coat; he fumbled with the sonic and Starlight picked it up

"Starlight!" the startled Doctor said before metal doors slammed shut

Starlight was left in the room; feeling mixed feelings

For one thing the Doctor was going to be put through what these people had been through

Two: He wasn't her Doctor

Three: Rutabaga

Starlight tried to calm herself down; but she felt uncontrollable rage that coursed through her

Her entire being began to convulse; she shook without any way to stop

[…]

The Doctor was strapped down on one of those tables; a machine went close to his face

"_This is our Timelord Factory; here is where we take the regenerations from timelords and use them as energy._" The voice explained

"You don't know what you're doing." The Doctor said, "You haven't for a long time."

Several workers were behind windows; all of them were in hazmat suits so he couldn't tell who they were

"_We have no intention to kill Timelords_" the voice continued, "_But if they have no regenerations left after a while they just die._"

"Well then" the Doctor felt sick in his stomach, "Then what are you going to do with me? I don't have any left."

"We are not fools" one worker said, "They all say that."

"Wait!" the Doctor protested, "This could be worked- Aggh!"

The machine was turned on; trying to absorb the Doctor's life energy

Then the walls exploded

Now I could say they went off their hinges; but I mean _exploded_

Shrapnel went everywhere and the smoke was thick

The Doctor was left strapped down so he couldn't get a good angle of what was going on

"Starlight! Is that you?" the Doctor called

There were screams through the smoke; the screams of dying people

Horribly dying

The Doctor stiffened; what was going on back there

A pony came through; her hair was black with blue tips

"I am _Midnight_" she said; flipping a lever

The Doctor felt the pain again; but with it came a rush

"You just want to get back! But killing me won't help!" the Doctor said

Then the straps released; he dropped to the floor

Midnight's mane went back to normal and Starlight fell to the floor

"What?" the Doctor scanned her and picked her up

"A magical residue" the Doctor thought out loud, "This residue seems to be very potent."

He went back into the TARDIS

Then he sat back; putting Starlight in one of the bedrooms

* * *

"Right; I guess I can inspect the TARDIS core while I'm sitting around." The Doctor went into the woodwork of the TARDIS

Inside everything seemed to be alright; however he seemed to be getting terribly low on power

Except for, "What's this?"

The Doctor then picked up a small metal device; it was attached to the TARDIS travel matrix

It wasn't Equestrian technology; or Covenant; it was closest to a mix of Dalek and Cybermen

The Doctor took it up to the top of the TARDIS console; with tech like this he could make something useful

"Maybe a sonic upgrade or even a perception filter!" he said; excited with science-y things

So he got to work; those components were heavily complex; similar to Timelord technology more than anything

Then it hit him; it _was_ timelord technology; that and Dalek and Cybermen

It was many technologies all cobbled together; they seemed to be for multiple purposes

The Doctor worked quickly and efficiently; making a perception filter along with having spare components for later

Then he hit the TARDIS handbrake; going off to an adventure in the unknown

[…]

The Doctor stepped outside the TARDIS and felt his gut drop

He had been here before; this _exact_ moment before; hastily the Doctor put a perception filter on himself and the TARDIS so if his past self saw it he wouldn't think anything of it

Then the Doctor decided to look around for nostalgia's sake

He walked through the dark alleyways of London; the moon high in the sky and the streetlights a ways off

Then he heard a scraping sound; shoes or metal

Or metal shoes

The Doctor followed the sound; going deeper into this deathtrap of London

He saw something glint in the darkness; he then bumped into what was casting it

He looked up and saw a cyberman; who peered down at him

"I believe this is where I run." The Doctor turned on his heel and dashed off

The Cyber freak didn't give up; no it chased him through the alleyways that existed

The Doctor rounded a corner

*WHAM*

Then he picked himself up and helped up the man whom he ran into

Then he froze

It was his past regeneration; his 12th to be exact

A leather jacket and dark brown eyes; a buzz cut alongside dark brown follicles

"What are you doing back here" the past Doctor demanded, "Nobody's supposed to be back here!"

"I'd ask the same question" the Doctor said, "What's your name?"

"Doctor John Smith" the past Doctor flipped psychic paper

It had an ID

"I'm Professor Anthony James." The Doctor said; flipping his own psychic paper

*Crunch Crunch*

The cyberman stood behind the 13th Doctor

He turned around and then Smith pulled him out of the way

"Run!" Smith shouted

And did he run; he ran alongside his past self like he never did

'I'm interfering with my own timeline!' he scolded himself, 'But did I have a choice…?'

Now that he thought about it he couldn't remember much about his past adventures as the 12th; besides the whole Equestria thing

Smith turned out into the streets; the Doctor followed him

"How do you manage to do that?" Smith asked

"Nearly get killed?" the Doctor asked, "I'm an astronomer; occupational hazard."

Smith laughed a bit; but didn't go much

Now the 12th Doctor is hard to impress; he's not exactly the guy you want as a judge in ANYthing; similar to the 5th Doctor

The 13th Doctor is a little more easily impressed; he's a stickler for new things; in that aspect he's like the 10th Doctor

(At this rate I might as well throw a story out where all 10-13 Doctors meet; let me know if you want to see that)

"You should probably leave" Smith suggested

"And leave behind this chance at an adventure?" the Doctor replied, "I'm not guessing so."

He reached into his pocket to grab his sonic when he remembered that Starlight still had it

Perfect

Now he had to play it cool; try not to let his past self know who he was; that might make a stable loop in time and keep reality in check

It's all wibbly-wobbly-timey-wimey like that

"These things are dangerous" Smith insisted

"I figured that out" the Doctor rolled his eyes, "But where's the fun in playing safe?"

The 12th Doctor got a glint in his eye, "You remind me of an old friend of mine."

'Like your past self?' the Doctor thought, "I get that sometimes."

"We should find a place to stay" Smith said, "You know any places around?"

"I'm not from around here but" the Doctor pointed, "There's a little inn over there."

The inn was called Little Inn

(You think I'm joking? Well I probably am.)

They walked in and got two rooms; then they settled in to sleep

[…]

The Doctor had a dream; it was what had just happened from the perspective of the 12th Doctor

He had made a stable loop so far; if he could keep it up then he might be able to pull paradox aversion

[…]

Starlight sat up in the TARDIS; looking around, "It was only a dream?"

She checked herself to see if she had everything; but what she found was a sonic screwdriver

"Oh no; this is the Doctor's…" she sighed and knew what she had to do

Starlight trotted outside the TARDIS; nearly touching a metal man

'Did the Cyberponies get anypony not really a pony?' Starlight thought

(Try it. Say that ten times fast.)

Then it turned around

[…]

The sun was rising and the Doctor sat up; deciding to make breakfast

Smith was working down with a map; he took the fish and chips the Doctor prepared and kept his eyes on the map

"So what's the plan Mr. Smith?" the Doctor asked

"Doctor Smith" Smith said, "We need to expel the Cybermen out of London."

"Well that may prove to be difficult" the Doctor said, "But what if we don't use force?"

Smith looked the Doctor up and down, "I like the way you think."

Together the two versions of the Doctor worked on the single cleverest plan in the history of plans

[…]

(Let me know if you think I shouldn't do the […] thing)

Starlight had bolted; the cyberman didn't even have time to acknowledge her, she ran hard and fast; trying to remain out of view of humans

'I just need to give the Doctor his sonic screwdriver; then I can go back to the TARDIS.' Starlight thought

Of course she ran right into him

[…]

The Doctor had taken the liberty to get back his sonic screwdriver and tell Starlight to stay in the TARDIS

So naturally it went wrong when she rounded the corner and slammed into him; knocking him off his feet

The wind knocked out of him; the Doctor stood up and nearly went into a panic; he hid Starlight in the nearby shadows

"Right perfect" the Doctor said; he took off the perception filter he had and put it on Starlight

"Now no one will think anything of you; unless you bring attention to yourself." The Doctor explained

"What about you?" Starlight asked

"I'll be fine; I already crossed my own timeline so I can't do much more damage."

Her jaw dropped, "You did what?"

"It was an accident" the Doctor said, "As long as he doesn't know it's me we'll be fine."

"Right" Starlight said, "Why don't we just leave?"

"We need to stop the Cybermen" the Doctor answered, "And I'm part of our plan."

"And that plan is?"

The Doctor leaned in and whispered the answer into her ear

"Are you insane!?"

"Quite possibly" the Doctor clapped his hands together, "Let's get started."

[…]

The CyberLeader was watching a screen; it showed the 12th and 13th Doctors

"This man is highly dangerous" he pointed at the 13th, "This man must be deleted." He pointed at the 12th

"We will assimilate the population" a cyberman said, "Then we will delete them."

[…]

The Doctor looked around; the sun was in the sky for mid-morning

"We should be able to get the supplies from this store" he walked inside

The store sold some basic piping and a goat head

"I'll take ten feet of PVC piping and that goat head." He said to the manager

"Alright" the owner said

ONE EPIC MONTAGE LATER

The Doctors looked at the contraption they had made

"Are you sure this'll work?" Smith asked

"Of course not" the Doctor answered, "Want to find out?"

"Right then" Smith looked around, "We need a lure."

"How about that metal thing?" the Doctor asked

Smith held up his sonic; it was the same one he had as the 11th

"You're good."

"I try my best" the Doctor took it, "We can slide this and hit the button."

"Do you know what it'll do?" Smith asked urgently

"No." the Doctor shrugged, "But it'll be one heck of a lure."

He hit the sonic; several light bulbs burst; power lines sparked and then they were in relative darkness

"What's the problem eh?" the Doctor shouted, "You want the Doctor well he's right here!"

"Delete Delete." A voice said; tromping towards them

The Doctor looked at him; it was the cyberman leader himself

"Careful Professor" Smith warned, "They're dangerous."

"No time for that" the Doctor said, "Hit it!"

He jumped; a hypersonic blast seared through the air where he had just stood; obliterating the cyberleader

"One problem" the Doctor said, "What about the others?"

Several more were tromping into the small intersection they stood in

"Now would be the time I say a cool catchphrase" the Doctor said, "But I don't have one."

"Try Allonsironimogi." Smith said, "A mix of Allonsy and Geronimo."

"Allonsironimogi!" the Doctor said; holding the sonic in the air

"You will be deleted"

"One thing about astronomers" the Doctor said

"Is that they are really clever" Smith said

"In foreign alien _tech!_" he hit the button

Several tubes came out of the ground; each one gave a hypersonic pulse and destroyed each cyberman

Then they felt the ground shake underneath them; a larger cyberman came out of the cobblestones

"Dear goodness" the Doctor said

"Come at me you big lug!" Smith threw a rock at it

When it turned around the Doctor jumped on it back; using the sonic to scramble its circuits

The metal giant stumbled and fell to the ground; then Smith cut a cable and a ton of rocks fell on top of its metal skull, crushing it

The Doctor stood panting; then he handed Smith back his sonic

"Well that was interesting" Smith said

"It was brilliant!" the Doctor commented

"So" Smith said, "What are you going to do now?"

"Probably go back to what I did before" the Doctor said, "Observe the stars."

"You could always come with me" Smith said

"I can't say yes to that" the Doctor said; then he took the 12ths hand, "Those you care for are gone; but they forever live on, in your memory."

Smith cocked an eyebrow and turned to leave

"And Doctor?" the Doctor said, "Don't lose sight."

Smith nodded and left

Starlight trotted behind the Doctor

"I told you we could handle it." The Doctor said

"You did but" Starlight looked around, "What now?"

"We go back to adventuring of course"

"_'we'_?" Starlight asked

"Yes, _we_." He handed Starlight a key, "You best stay with me."

Starlight smiled and they went back to the TARDIS


	3. Library Anyone?

One lone pony was in the library in Canterlot; the long day in the library wore him out. Luckily for him he was able to stick in the restrooms long enough to wait it out

But when he got out of the bathrooms nopony was around; the lights were out and he thought he saw a bone

"Weirdest thing that." He said

Then he felt like he was being watched; he turned and saw nothing but a shadow on the wall

'Great. Now I'm scared of my own shadow.' He put his hoof in it

And next thing he was a skeleton on the floor

[Dun nun nun nun; dun nun nun nun; dun dun nun nun! Dun dun nun nun!]

Skarfly as: The Doctor

StarlightWhovian as: Starlight

The Doctor landed the TARDIS; then he stepped out front

"Right; the royal Canterlot Library" he said, "I figured we could visit before getting home."

Starlight sighed, "Can I stay in the TARDIS?"

"Well if it suits you" the Doctor shrugged, "I just want to take a look around."

The TARDIS doors shut

The Doctor continued through the library

[…]

Two royal guards were deeper into the library; they were a mix of Lunar and Solar guards, both wore hazmat suits

"I don't understand what could have done this." A rookie solar guard said

"Maybe a parasprite attack." One lunar guard joked

"Knock it off you two" a female voice said, "We need to-"

*CRASH*

"Hey; I thought the area was restricted." The rookie said

"It is" the Lunar guard answered

*CRASH CRASH*

They saw a door heaving; then it broke open

There was a man on the other side, "I'm sorry am I interrupting?"

[…]

The Doctor looked at the trio of ponies; all wore hazmat suits

"Masks off" the one in front said, "We have a breather."

The guards took their helmets off; when the female pony did the Doctor felt his pulse quicken

"Twilight Sparkle is that you?" the Doctor asked; shocked

"Who are you?" Twilight asked, "And how do you know my name?"

The Doctor approached, "You seriously don't remember me?"

Twilight didn't move; but the guards tensed

The Doctor looked at her, she had wings and a horn; an alicorn the term was

"You really don't remember me." The Doctor said; sadness in his voice

This couldn't be her past self; this version had wings when her past self didn't

"I can't say I do" Twilight said, "What's your name?"

"Oh. I'm the Doctor." The Doctor said

"Doctor who?" the rookie solar guard asked

"It's just the Doctor" the Doctor said

"Is that even possible not to have a name?"

"It is my name" the Doctor said

"Never mind that" the Lunar guard said, "What are you doing here?"

"If this place is under lockdown then that leaves one question" the Doctor looked around, "What happened here?"

"You're not supposed to be here" Twilight said

"Well I am and I've got questions" the Doctor countered, "Where are the workers? I don't see blood."

"That's what we're here to find out" the rookie answered, "It happened late at night."

"Hmm." The Doctor thought about it for a moment, "Don't go into a shadow; not a hoof. If this is what I think this is we're in trouble."

The Doctor took out his packed lunch; he took out a chicken wing

"Is that meat?" the lunar guard asked

"My entire species are omnivores" the Doctor said, "Yes it is."

Then he tossed it into the shadows

He blinked

And then it was a bone; hitting the ground

"This is in no way good." The Doctor turned around, "Alright; we're in lots of danger. And I'm the only one here who knows what he's doing."

"We need to know what killed the workers" Twilight persisted

"There's your problem" the Doctor pointed at the bone, "Vashta Nerada. They eat meat, microscopic and very ravenous."

"They _ate_ the workers?" the rookie sounded scared

"Naturally" the Doctor said, "And now you're in the same danger."

"What about the ponies outside?" Twilight asked

"This area's been restricted in a time bubble" the Doctor answered, "We're alone in here, unless we can get to my ship."

"Ship?" the rookie inquired

"Let me know if you see a tall blue box and we'll be fine." The Doctor said, "Now let's go."

"You're not the one in charge" Twilight said

"Listen Twilight-"

"_Princess_ Twilight." She corrected

The Doctor got in her face, "You don't know what you're up against; I'm from another planet where I've seen things like this daily. I've fought and saved billions of lives countless times and I am the one who's going to get you out of here alive, only if you let me."

Twilight rolled her eyes

"Now then" the Doctor said, "Normally I would say their weakness but they don't seem to have one. We can do one thing: run."

"Run where?" the lunar guard asked

"Away from here; let the Vashta Nerada starve to death." The Doctor answered

"Tall blue box. Got it." The rookie said

"Right now we should get going" the Doctor took out his sonic, "Allonsironimogi!"

[…]

"This truly is a massive library; built with hooves of all things" the Doctor admired, "Still easily a disaster area, you're not too different from humans in architecture after all."

"Can we focus on getting out of here alive?" Twilight snapped

"Fine by me" the Doctor said, "Just avoid touching any shadows."

"Why?" the rookie asked

"You saw the bone rookie" the Doctor said, "Any shadow could have Vashta Nerada in it."

"How many?" the lunar guard asked

"Not every shadow but any shadow" the Doctor kept a crisp pace, "Don't let your shadows cross and make sure you have as many shadows as you do light sources."

"Doctor?" Twilight asked, "I have two shadows."

The Doctor sighed, "Then they've latched on to you."

"What's going to happen to me?" Twilight asked

"I can try to save you but I can't be sure it'll work." The Doctor said, taking the sonic, "Allonsironimogi!"

He used the sonic on the shadow, at the base as to disorient them into leaving

The shadow broke off and went into the darkness

The Doctor sighed explosively, "That was close-"

The skeleton of Twilight Sparkle hit the ground

"Twilight!" the Doctor knelt beside her bones, "No! This can't be happening!"

"She's dead Doctor" the lunar guard said, "We should leave her body in peace."

"I'm sorry I couldn't save you Twilight" the Doctor said, "Now I need to get the others out."

The Doctor stood up and motioned for the door, "Let's go. We shouldn't stay here."

[…]

The Doctor opened the door and the TARDIS was on the other side

"Now we can get out of here" the Doctor turned around

And two skeletons were on the floor

"Oh come on!" the Doctor protested, "We just about escaped with our lives and you decide to come at us like that?"

The Doctor sighed and went inside the TARDIS

Then he flipped a few switches and took off, 'I'm sorry Twilight…'


	4. Magical Menace (Univore part 1)

The Doctor decided it was best to go home while he could; he flipped the switch and landed the TARDIS

Then the TARDIS jerked to the side; the Doctor held on as he was hit with a time rift

"What was that?" Starlight asked

"Trouble" the Doctor answered as the TARDIS went off course

Starlight was flung to the side, the Doctor clung to the handrail

"What's going on?" Starlight asked

"We're entering a universal debris field" the Doctor said, "A universe used to be here!"

"Well which one was it?"

"Mine."

The silence was only evidenced in the TARDIS rumbling

"I'm sorry" Starlight managed to say

"Don't be" the Doctor said, "At least we weren't inside when it happened."

"So what now?" Starlight asked

* * *

Meanwhile in Equestria something was going wrong

Several unicorns in Canterlot had been going missing recently, completely vanishing. Not even their neighbors know what happened to them

(Get it? NEIGHbors? Anybody? Crap…)

Anyways Twilight and her friends were visiting the capital when things took a turn for the worse

Both Celestia and Rarity went missing

"What are we going to do?" Rainbowdash asked

"We don't have anything that could lead us to them" Twilight said; her wings furling in frustration

(Yes Twilight is an alicorn. Spoiler for season 3 finale.)

"And Canterlot is too big fer us to search on our own." Applejack complained

"Girls" Fluttershy said, "Why don't we call?"

Twilight took out the phone; it was the same cellular phone that the Doctor gave her in case she ever needed his help

"Are you sure Fluttershy?" Twilight asked, "It's only for emergencies."

"To hay with emergencies!" Rainbowdash said, "The princess is missing!"

"Right" Twilight conceded; then she hit the speed dial

The TARDIS phone began to ring; the Doctor picked it up

* * *

"Hello there." The Doctor said, "This is the Doctor."

He listened, "Twilight! Good to hear from you, the princess is missing? Now that won't do at all. We're on our way."

The Doctor almost touched the handbrake; but before he could he was thrown back as the TARDIS started to travel

In the dark alleyways of Canterlot a duo of ponies who were working at it

"Come on Derpy. We need to get this done quickly." The brown stallion said

"Alright Doctor" Derpy said, "We're in danger of him coming here."

"We're doing more than that" the pony version of the Doctor said, "We're bringing him to us."

Then he flipped the switch on the contraption

* * *

Twilight heard the unmistakable sound of the TARDIS, she galloped outside and saw the TARDIS

It was barreling towards the city

"Incoming!" Twilight said; hitting the floor

The TARDIS flew right over her head, the wind whipping up her mane

The TARDIS made a U-turn and landed in the courtyard; the Doctor stepped out

"Somebody call a Doctor?" he asked

"Doctor" Twilight said, "You came quickly."

"Well I can't leave a friend waiting" the Doctor answered, "Right so let's get started."

"Wait wait stop." The Doctor said, "You have wings."

"Well I became an alicorn recently" Twilight said, "I can't fly very well."

"Right then" The Doctor said, "Come along."

The Doctor walked into the throne room; the air was cold without the care of Celestia in the room

Luna waved

"Let's take a look around and see if there's a pattern." The Doctor said

"Where do we start?" Starlight asked

"All the ponies missing were unicorns" Luna said, "Except Tia, who's an alicorn."

"So what's the power source of this universe?" the Doctor asked aloud, "It's not electricity, so it must only be-"

The Doctor clapped, "Magic!"

"What about magic Doctor?" Fluttershy asked

"It's related to the kidnappings" the Doctor said, "If magic is power then why make it public by taking the princess…? Aha!"

Everyone jumped when he exclaimed this

"What has more powerful magic than a unicorn?" the Doctor said, "an alicorn!"

Luna gave him a look, "Does that mean Twilight and I are at risk?"

"Almost definitely" Starlight said

"So what do we do?" Rainbowdash asked

"We need to mount a defense" the Doctor answered, "A group of guards. None with magic."

"That'll keep you safe for now" Starlight said to Twilight, "The Doctor and I can figure it out from here."

"What about us?" Rainbowdash asked

"There are three of you correct?" the Doctor asked, "Two of you will protect Twilight and one will stay with Luna."

"Ah'll stay with the princess" Applejack said, "Ya'll protect Twilight ya hear?"

(I may or may not be overdoing it for Applejack's voice)

"Alright Applejack if you're sure." Fluttershy said

"Now first things first" the Doctor said, "Starlight let's go investigate."

"Hold on Doctor" Twilight handed him a badge, "This will let you in as an official Equestrian Detective."

"I like the look" the Doctor said

It was a gold plated badge with the Equestrian symbol on it

"And you get this" Twilight handed Starlight a vial, "It's spare magic in a bottle."

"Nice to meet you Twilight" Starlight said

"You too" Twilight said

The Doctor strode out of the castle gates; Starlight following him

* * *

Doctor Whooves was watching from the shadows, "So he found Starlight, brilliant."

"When do we talk to him?" Derpy asked

"When the time is right Derpy" Whooves said

* * *

The Doctor started first by talking to the relatives of the missing ponies

"Would you mind if I took a look inside?" the Doctor asked a mare

"Please bring him back if you can" the mare said, "FancyPants doesn't like being in danger."

"Well I do and that's why I'm here." The Doctor went upstairs

The room seemed clean enough; no overturned furniture. The paintings were still on the walls and no footprints

The Doctor took out his scanner and scanned the room; his sonic blipped

"The time vortex opened in this room" the Doctor said, "That means someone warped him out. No struggle."

"Where is he now?" Starlight asked

"Let's go to the room of the most recent kidnapping" the Doctor said, "Maybe we can trace the signal."

The Doctor rushed through the town; on his way to the castle

"We'll be able to find someone at least." The Doctor said

The Doctor walked into the room where Rarity had been staying; the sonic made a few more blips

"There was certainly a time vortex opening in here" the Doctor said, "And if I'm correct"

He looked under the bed, a hole was there

The Doctor took a deep sniff

"Yep. There's a time hole right here." The Doctor said

"What's a time hole?" Starlight asked

"A place in time where the vortex opens at random times." The Doctor answered, "It always leads to the same place each time."

"So unicorns have been falling into the vortex?" Starlight summed up

"No. It can't only be unicorns, this was all planned." The Doctor said, "My guess is someone has time travel here and has deliberately left traps for everyone who went missing."

"I'm sorry" a voice said, "Authorization please."

The Doctor turned and saw a unicorn, her eyes were brown and her mane was a lighter brown, her flank had no cutie mark nor did her eyes glint with any intelligence

"The word authorization doesn't belong in this universe" the Doctor said, "What are you?"

The mare let out a bloodcurdling cry; out of her mouth shot a strange light that enveloped Starlight

"No!" the Doctor cried but it was too late; they were gone

A guard rushed in, "Is something wrong here?"

The Doctor took a deep breath, "Something is very wrong here. I need access to the Princess Celestia's room."

"For what purpose?" the guard asked

The Doctor flipped the badge, "Investigation. I'm the Doctor and the Doctor is in."

Whooves was down in the courtyard, "It seems that he's getting closer."

"When do we go in?" Derpy asked, "He needs our help."

"When he truly needs us we'll know." Whooves said

The Doctor was in Celestia's room, there was nothing out of the ordinary but the Doctor felt it

This was where they went

The Doctor used the sonic on the paintings, only one clicked

It was a painting of the infamous blue box, the TARDIS was in the throne room with a picture of the 12th Doctor

"This is too good for a painting" the Doctor said; reaching out for the painting

There was another bloodcurdling cry; the Doctor rushed out of the room and into the throne room

"Not on my watch!" the Doctor used the sonic without thinking

The bloodcurdling cry was coming from one of the guards; the guard's head exploded into circuitry

Luna was gasping with shock

"Well then" the Doctor said, "That one was close."

"Thank you Doctor" Luna said, "It seems that they are not satisfied with my sister."

"How many alicorns are there in Canterlot?" the Doctor asked

"Four total" Applejack said weakly; from the floor

"Luna and Twilight are protected and Celestia's been captured" the Doctor said, "Who's the fourth?"

"Princess Cadence!" Luna said, "She stopped by for a visit!"

"Shining Armor can keep her safe" Applejack said, "Where's Starlight?"

"Wherever Celestia is" the Doctor said

Twilight and the others raced into the room

"What happened?" Rainbowdash asked

"One of them was disguised as a guard" the Doctor said, "Nearly got Luna."

"Applejack!" Twilight rushed to her fallen friend, "Are you okay?"

The Doctor started to work on the components, "A pilot fish."

"A what?" Rainbowdash asked

"Something far bigger is here" the Doctor said, "And they need energy. Think!"

The Doctor whipped out the sonic and scanned the broken droid

"I can trace the signal from here" the Doctor said, "You keep Twilight and Luna safe."

"Where are you going?" Rainbowdash asked

"Starlight needs me" the Doctor said, "I can't keep her waiting."

"Are you sure Doctor?" Luna asked

"As sure as I can ever be." The Doctor answered

"Well you might need help with that" a voice said

The Doctor turned and saw a brown coated stallion with an hourglass cutie mark

"Hello there" he said, "They call me the Doctor."

* * *

Starlight woke up, she was strapped down and there seemed to be something on her horn

"Doctor?" she called; her voice raspy

Only silence answered her

"Help…"

TO BE CONTINUED


	5. Seeming Peace (Univore part 2)

The Doctor was taking a careful look at the stallion; seemingly unfazed

"So you're the Doctor that Starlight traveled with." He observed

"I see you found her, I'll ask more later." Whooves said

"We need to find the unicorns." Derpy added

"Right then" the Doctor said, "Let's scan for magical energy, where there's the most we could find them."

The Doctor took out the sonic; then put it away

"It must be a dampened signal, I can't find it." He said

"Where do we go then?" Derpy asked

"To the only place they could hold a couple dozen unicorns." Whooves said, "Somewhere close to the castle."

"Like under it perhaps?" Luna added

"Turner." Twilight said, "You're an alien?"

"Oh yes" Whooves said, "And Turner is not my real name."

"Let's hurry" Derpy said, "We can't just stand around."

"Well then" the Doctor said, "Let's go."

The Doctor and his two compatriots walked out front of the castle

The Doctor hunched over suddenly, grabbing his chest

"My universal ties have been broken" he said, "I don't know how long until I fade out."

"Not yet Doctor" Whooves said, "Starlight needs you."

"Right then" the Doctor struggled to keep walking, "We should hurry."

"Are you going to be alright?" Derpy asked

"I'll have to be" the Doctor answered, "We need to get moving."

And the trio had to race the clock, to find the unicorns before everything went down the crapper

And yes I just said that

The Doctor threw up his hands, "I don't know what to do."

"Try focusing" Whooves suggested

The Doctor took a deep breath and closed his eyes, feeling the shift of the universe flow through him

'_You know where you must go_'

"Let's go to the castle" the Doctor said, "I may have an idea."

Then they went to the castle, Whooves looked at the Doctor oddly

"They may not be as safe as we thought" the Doctor thought aloud, "They may be part of something worse…"

"You said your ties were broken" Derpy said, "Does it have to do with that?"

"Exactly, my universe was gone and I think I know why."

The Doctor walked right up to Celestia's throne, ignoring the shouts of the guards

He used the sonic screwdriver on the top; a puzzle appeared and, with his 1,223 year experience, was solved quickly

There was a rumble, the throne divided into two pieces, and a staircase downward was revealed

"They must be down there" the Doctor said

"Why there?" Derpy asked

"Where else hide something so dangerous?" Whooves asked, "Somewhere nopony dares to go."

"Under the princess's backside." The Doctor joked

The three ponies descended, followed by two guards

"What could be down here?" Whooves asked aloud

"The one thing that can survive in the Void between Worlds" the Doctor said, "The only creature that can devour a universe."

"You can't mean…?" Whooves implored

"It very well may be." The Doctor answered, "We're too slow."

They got down to what appeared to be a chamber, metal floors and high ceilings, they were on a walkway, several hundred containment chambers sat there

"I have a bad feeling here" Whooves said

"As do I" the Doctor said, "We may have stumbled into-"

The ground rumbled, a warning growl

"Hey there Univore!" the Doctor called out

Two eyes appeared [purple, with green irises], a great sharp toothed maw opened

"**_Doctor…_**"

"That's me, I'm the Doctor." He said, "But you tried to kill me, worse you tried to harm my friends and _I_ _will not have that._"

"**_This universe is my prison, I take my rations._**"

"These are sentient beings!" Whooves said, "They are far from rations"

"This is everypony's home!" Derpy added

"You know, you almost had me when you ate my universe" the Doctor said, "But being dragged here was a huge stroke of luck, I survived."

"You know that's who I am" the Doctor continued, "I'm the Survivor, everything and I'm still here, 1,223 years old and still going strong."

"**_You're weak, the universe shattered easily_**" the Univore countered

"I've accepted that" the Doctor said sharply, "It's the fact that you tried to hurt my friends that get me."

"1,223?" a guard whispered

"I'm not just any man" the Doctor said, "I'm the Doctor, a timelord from the planet of Gallifrey! A major role in the Last Great Time War!" he paused, "And you just made me very angry."

"**_This is my cage, why not let me out?_**" the Univore grinned widely

"Because you can't eat it from in here" Whooves said, "Only when you're outside."

"So I'm afraid we're at a standstill." The Doctor said

"**_Get me out of this universe and I will not get in the way_**" the Univore claimed

"I have an idea" Whooves said, "Doctor, your sonic?"

The Doctor handed it to him, "I can use this to create a hypersonic wave, shattering all of this."

"I have questions" the Doctor continued, "Why take the princess everyone was watching? There were several not being heavily guarded."

"**_I did what was necessary, my turn._**"

The Doctor crossed his arms

"**_Why do you still have hidden energy?_**"

The Doctor looked himself over, "I shouldn't."

"**_DON'T LIE TO ME!_**" the Univore roared, "**_I AM NOT ONE TO ANGER!_**"

"You know?" the Doctor turned to Whooves, "Hit it."

Whooves turned on both sonics, and due to them being the same model, it created a hypersonic wave, breaking the containment chambers and freeing the unicorns within

The Doctor broke into a dead sprint, ignoring the pain in his abdomen and hitting a button

"I hope you like another universe!" the Doctor said, hitting it

The Univore lunged, the Doctor leaped and landed on a ponies back

"We must hurry" Celestia said, "Come Doctor!"

The large mass of unicorns made for the exit, Starlight met up with Whooves and Derpy on the way

"Where's the Doctor" Starlight asked

"He's on his way now come on!" Whooves said

They went up the staircase and made it to the top, all funneling out into the throne room and out the doors

The Doctor climbed off the princess's back, "I appreciate the ride."

"You're welcome" Celestia said, "After all you came in our time of need."

"Doctor!" Starlight ran to him

"Good to see you" the Doctor said, "Maybe now we can go on an-"

He grabbed his chest and fell over, hitting the floor

"What's going on?" Celestia asked, Luna by her side

"He said he no longer had a universal connection" Whooves said, "He's fading out of existence."

"I won't let him!" Starlight fumbled for something in her pocket

She pulled out the bottle of spare magic that Twilight had given her, injecting it into the Doctor

"What'll that do sister?" Luna asked

"If I'm correct" Celestia said, "He may pull through with it."

"Either way he'll die" Whooves said, "He's out of regen-"

He stopped, a yellow energy was coming off of the 13th Doctor, flowing through him and encasing him

Then he started to regenerate


	6. Celestial Changes part 1

The castle was silent as the timelord floated into the air, out of view behind the yellow haze

His regeneration stopped suddenly, he writhed on the floor, seemingly splitting in two

The Doctor cried out in pain, his very being was being torn apart

"The magic wasn't able to stop it!" he said in between gasps of agony, "I'm still done for!"

"What do we do?" Twilight asked

"I'm dying everyone" he said, "Let time take its course."

"We can't let that happen!" Rainbowdash protested

"Well what do we do then?" Starlight asked Rainbow

"I don't know; something?"

Then all attention was back on the humanoid on the floor, or should I say huge mess on the floor?

The Doctor backed up, looking down at a stallion with a dark green coat, a brown mane and an hourglass cutie mark

"That hurt, a lot." The Doctor commented

"Doctor! You're okay!" Starlight gave him a hug

"I'm sorry have we met?" the Doctor asked

Starlight looked at him; he didn't show a single sign of recognition

"Doctor, you know me. Starlight?" she asked

"Can't say I do" the Doctor said, scratching his head, "My memories seem to have been messed with."

"Then who-" Starlight looked down at the green pony who was standing up

"Starlight it's great to see you!" he said, "This is what happened when the magic took effect."

"It split into two beings" Whooves said

"Precisely" the green pony said

"If you remember me" Starlight looked at the Doctor, "Why doesn't he?"

"Well the memories most likely split" the green stallion guessed, "It's not often a timelord splits in two."

"So you're a timelord?" Twilight asked

"Me? No I'm not" he said, "Just a pony; a result of the split."

"But a pony with the mind of a timelord" Whooves said

"This is all well and good but" the Doctor said, "Aren't we done with the threat?"

Then he stopped and looked over the princess

"Well" he said, "You're giving me a weird look"

"You just split into two beings" Celestia said, "That shouldn't be possible."

"Neither should timelord plus magic!" the green pony said, "I guess I'm John Smith?"

"How about Clock Crasher?" The Doctor asked

"Why Clock Crasher?" Derpy asked

"Well it's to go with the hourglass, and the fact that we like to 'crash' in many places." The Doctor explained

"It's time for a party!" Pinkie Pie interrupted, "The author is having a hard time keeping all these characters with speaking roles!"

(She has no idea)

"I think I do" Pinkie said

The three versions of the Doctor looked around; trying to place exactly who she was talking to

"Right then" the Doctor said, "Party time?"

That night the Doctor had shown up and saw the crazy party that Pinkie Pie had set up, there were streamers EVERYWHERE. Pink Blue you name it, all colors of the rainbow were on the walls that night

"Hey Doctor" Twilight trotted up; wearing her gala dress, "How are you?"

"Well this party is very…" he tried to place the right word, "Energetic."

"Whenever Vinyl shows up; it's bound to be." Twilight said

"You didn't forget Starlight did you?" Twilight asked; eyeing him judgingly

"Of course I didn't" the Doctor said; looking out to see Starlight, "But she'll be happier with Clock Crasher; she can't stay with me."

"What are you going to do now?" Twilight asked

"Nothing, everything. I'm not sure yet, only one way to find out."

"Will you come back?"

"I always do" the Doctor shrugged, "I guess we can enjoy the party first."

The Doctor didn't mingle with the partygoers much; it was just something he wasn't used to

Instead he tried to figure out the princess, why was she so hostile in the first place? It would make sense if she knew him _personally_. Which she didn't at the time; which means she met him at one point and the meeting didn't go well at all.

This whole situation was worth looking into, 'As soon as this party's over I'll go and take a better look.'

"Princess Celestia may be a problem" a voice said beside him

The Doctor turned and saw Clock Crasher

"She's hiding something" he said, "You should look into it."

"Take care of Starlight while I'm gone?" the Doctor asked

"I will" Clock Crasher looked at him, "Find out what happened, and take care of it."

"Something is wrong" the Doctor agreed, "And I'm going to fix it, you can count on that."

The Doctor walked into the TARDIS and took off

The Doctor was standing by the console; the silence pervaded throughout his being as he was the only creature in the small spacecraft

"Right" the Doctor pulled up the picture from the Halo ring

It was strange text that he had found, why did he stop?

This wasn't forerunner, it was Old High Gallifreyan

Here's a translation:

_In the shadows_

_Under the skin of the trusted_

_Lies an evil beyond those faced_

_For a lone wanderer to fall into its trap_

The Doctor sighed, "This is bound to not end well."

The TARDIS beeped

The Doctor remembered exactly what he did to stop the Univore, it wanted out of the universe. It tried to cause a hole in it to escape, however the Doctor had tricked it and sealed it inside a universe it could never escape.

The TARDIS started to shake

"Ah, we're nearing the universal walls" the Doctor said, then it happened

The TARDIS flipped, flopped and flung the poor Doctor around the room

"We bounced off the wall?" the Doctor sputtered; looking at the scanner, "This is very bad, very very bad!"

The console broke out with flames, smoke spewed and the Doctor covered his face with his coat sleeve

[Dun nun nun nun; dun nun nun nun; dun dun nun nun! Dun dun nun nun!]

Skarfly as: The Doctor

On the planet below a storm was brewing, a young mare was in her house in the late evening

Her coat was a mint green, her eyes were yellow and her cutie mark as a lyre

By now you should know this mare was named Lyra, and she was in the Celestial held town of Ponyville

Over the last few months there had been a war between the two princesses, each had a side

The New Lunar Republic

And the Celestial Empire

Lyra was drinking tea, thinking about the strain of war, how everypony had to choose a side

*WHOOSH WHOOSH*

Lyra had been told to listen for that sound, if the Doctor arrived he couldn't help the Lunar Republic or the war was practically lost

Lyra galloped outside, careful not to wake her sleeping roommate Bon-Bon

She looked around for the blue box, seeing nothing. But when she looked into the sky she saw it, coming down at ridiculous speeds

It flew right over her head, landing in the park nearby her house

Lyra approached slowly, it was half buried in the ground

The doors opened and smoke poured out, a man's hand gripped the edge and hauled the rest of him out

The Doctor coughed like crazy, then stood up unsteadily

"Well I have a headache like you wouldn't believe" the Doctor said, holding his bleeding skull

"Are you alright?" Lyra asked

"Well I think I have a concussion" the Doctor said, "Maybe a cup of tea might help-"

*BOOM*

A series of explosions went off, unluckily for the Lunar Empire the Doctor arrived right before a serious bombing run

And now he was in the middle of it

The Doctor reacted, he ran into Lyra's house and grabbed a metal bowl, then he attached the sonic screwdriver to the bottom

"And this is why that was a bad idea" the Doctor said

Then he used the bowl sonic contraption to send out a sonic wave, it knocked a few pegasi out of the air before they retreated

Lyra approached the Doctor, who sank to the ground with his back to her wall

"What was that?" the Doctor asked

"It was the New Lunar Republic" Lyra said

"New Lunar…?" the Doctor coughed, "When did this happen?"

"A few months ago" Lyra answered

The Doctor stood up, "We're having a talk, inside. Now."

Lyra followed the Doctor inside her house, the other ponies looking at the craters by the bombs

The Doctor sat down and took a sip of his tea, "Now then."

"What war?" Lyra blurted

"The war that involves the New Lunar Republic." The Doctor said calmly, "When did this happen?"

"I don't think that-"

"What happened?" the Doctor repeated

"It started when Princess Luna left the kingdom" Lyra sighed, "Princess Celestia refused, said Luna had no right, and Luna wanted to be alone like this so badly… War sparked."

"Right then" the Doctor said, "Anything else?"

"Even the elements have been divided, Twilight Fluttershy and Applejack are with the Empire" Lyra looked away, "Rainbowdash Pinkie and Rarity are with the Republic"

The Doctor put his hand to his chin, "Any other item of power users?"

"Well Princess Cadence and Captain Shining Armor are fighting."

"Something's off here" the Doctor said, "Something in the air, can't you taste it?"

Lyra shook her head

"It's staring me in the face!" the Doctor slammed his fist into the table, "What's going on here?"

* * *

A lunar guard rushed into the room, they were currently in the abandoned castle of the Everfree Forest

"Princess" the guard said, "The box has been seen."

"Where is the Doctor?" Luna asked

"He was nearby" the guard said, "But something unfortunate occurred."

"What is it?"

"It was seen during the bombing run" the guard cringed, "And the Doctor fought a few of our bombers."

"We need to get him here" Luna said, "Without him this war is lost."

The guard nodded

The doors opened and a few mares trotted inside

"Princess" Cadence said, "What do we do if he helps them?"

"The Doctor has fair judgment" Luna said, "If he chooses them then our cause was not noble."

"Maybe we can torture them." Pinkie Pie wasn't really herself, as evidenced by her straight mane and attitude, "It's a great pastime."

"If he chooses them then I'll take care of him!" Rainbowdash said; pumping her hooves

"The Doctor is not one to rile" Luna said wisely, "What he lacks in strength he makes up for in his brain. The marvel of a timelord."

* * *

Twilight was currently speaking with Celestia

"What are the timelords?" Twilight asked; while in the middle of her studies

"They are the oldest race in the universe" Celestia admitted, "Far older than I am, they mastered the art of time travel. I thought they had all been killed but evidently I was wrong."

"Older than you?" Twilight pondered, "How old is the Doctor?"

* * *

The Doctor walked through the streets of the decimated Ponyville, the bombs had been rather powerful

Several ponies had looked at the Doctor in shock, some in fear, and even more in admiration

'I must have gotten famous quickly' the Doctor noted

Lyra trotted up next to him

"Doctor" Lyra asked, "Why is there only one of you?"

The Doctor was silent for a moment

"They're gone" the Doctor said quietly, "All of them, it's just me now."

"But what happened to them?"

"The Last Great Time War happened" the Doctor left it at that

He entered Town Hall

"Where is everybody?" the Doctor asked

"Everypony has had their best friends turned against them" Lyra said, "Even my friend Bon-Bon was-" she choked back a sob

The Doctor put his hand on her neck, "I'll fix this, the sooner we figure this out the sooner we can bring things back to normal."

Lyra smiled, "So we're both in this?"

The Doctor grinned, "If you're up for an adventure."

Together they interviewed several ponies, each one showed an extreme anger towards the Republic

"I think I'm starting to figure this out" the Doctor ran his hand through his hair, "C'mon, we're going to the Everfree."

Lyra uncertainly followed him over the path to the forest

"Are you sure about this Doctor?" Lyra asked finally

"Once we hear both sides of the story will we figure this out" the Doctor answered, "Then I can choose."

They didn't even have to worry about finding them inside the forest, before they got inside they were stopped by a Lunar Guard

"Halt! You have been requested to be seated with the princess." the guard said

"Why else would we be here?" the Doctor countered

"And of the mare?"

"She's my assistant" the Doctor crossed his arms, "It's both of us or neither of us."

"Oh let them pass" Luna said, "I need to speak with them."

The guard lowered his spear

"Now then Doctor" Luna said, "Follow me."

The Doctor and Lyra walked through the untamed forest, the taste in the air was stronger

They passed several ponies, on one end there was an elderly mare with an apple pie cutie mark training some jars

On another end there was a little filly with a red mane and a yellow coat, she trotted up to the Doctor

"Hey, aren't you that Nurse everypony has been talkin bout?"

The Doctor laughed, "It's the Doctor, what's your name?"

"Ah'm Applebloom!"

"Nice to meet you Applebloom but I have somewhere to be." The Doctor said

Then they found the castle, it was old and in ruins. However after the hard work of the Lunar Guards it was within working conditions

"An interesting choice to be sure" Luna looked at the Doctor, "You see why we need your help."

"I think we have a bit to talk about Princess." The Doctor said

They made it to the old War Room

Luna sat down, Lyra did the same and the Doctor stood

"What exactly are you doing here Doctor?" Luna asked, "Weren't you going home?"

"I tried to exit the universe" the Doctor bit the inside of his cheek, "But I bounced off the universal wall, I'm stranded here."

"Well you have friends here" Lyra pointed out, "They can help."

"Not with this war" Luna corrected, "And we need to finish it."

* * *

Celestia was looking over the weaponry she had stashed, it had been here since the Doctor's first appearance in Equestria, she saw the iconic eye-piece and the blaster

She was looking at Dalek weapons

TO BE CONTINUED


	7. Celestial Changes part 2

The Doctor clutched his chest and pitched forward

"Doctor?" Lyra caught him as he fell

"The magical energy of the spare magic is fading, letting my body take back its hold on my place here" the Doctor explained; still shaking from the fall, "It's perfectly normal with a regeneration-ahh!"

The Doctor swallowed; and sat down on the chair

"Doctor, I have grave news" Luna said, "We may have a Dal-"

"Princess!" Rainbowdash trotted in, "Did he choose yet?"

"Rainbowdash, this is no time for there to be a rush. He is not hostile and even has not chosen yet." Luna said

"Sorry Princess" Rainbowdash said, "It's been a bloody year."

"Year?" the Doctor sat back, "I landed on this end of the century! I'm getting better at crash landing."

Lyra looked behind Rainbowdash, "Bon-Bon!"

Bon-Bon came out from behind the cyan mare and gave Lyra a hug

"You survived the bombs!" Bon-Bon smiled, "The park is right by our house, how did it stand?"

"By me" the Doctor said, "A little sonic resonance and a bowl, you get a sonic pulse that I used to save a few casualties."

"Which by the way, I am not happy about." The Doctor finished

"It is simple warfare, we take the closest area, and then move on." Luna defended

"Well before I choose either side I'm planning on going to talk with Celestia and whoever wants to come with me, feel free to." The Doctor gestured broadly

"This is not a wise decision, Celestia tried to kill you before." Luna warned

"And I didn't die, I cut it close that's how I roll." The Doctor said, "Now as I say, Allonsironimogi!"

The Doctor walked out, a small little diplomatic party following him

Of course you know that didn't end well

Halfway to Ponyville they had met an oncoming war party, and fighting broke loose, here's how

"Doctor do you see that?" Lyra asked

"See what?"

A laser beam flew past them

"Oh" the Doctor smiled, "Yeah I see that."

"Go Doctor, and attempt to make peace." Luna said

The Doctor walked forward, Celestia looked at him

"Greetings Doctor."

"Hello, I see you're planning on invading?" the Doctor asked

"I wonder, why are you here?" Celestia asked

"Well it's complicated but I'm glad I am" the Doctor crossed his arms, "I think I deserve to hear your side of the story."

While the Doctor prepared the tea the tensions in the room were high, they couldn't decide on a meeting point so the Doctor just decided they'd talk in Ponyville

The Doctor sat down, looking to each of their faces

"Now then, what exactly was Luna after that you wouldn't give her?"

"It was…" Celestia paused, "She wanted more freedoms."

"What kind of freedoms?" the Doctor pressed

"She wanted there to be a celebration for all of the princesses" Celestia said, "But something went wrong."

"What was it?" the Doctor said, "Tell me!"

"I don't know it just…" Celestia put her hoof to her head, "Something… it hurts…"

Princess Luna collapsed

"What is this?" the Doctor put his hand on his forehead

"Doctor?" Lyra looked at him

"I knew something was off" the Doctor hit his head multiple times, "But I was so blind to it! Something in the air is working to make everyone angry and unreasonable!"

"Why aren't you and I affected?" Lyra asked

"It must be the fact that I've not been here long and as for you, I have no idea." The Doctor sighed

Celestia stood, "I think we should leave."

But before they could an earthquake quaked the earth

(See what I did there?)

"Everyone out of the library!" the Doctor ordered, "Let's go!"

The group rushed out, a huge crater made up a large amount of Ponyville

"What happened?" Celestia asked

"I don't know" the Doctor said, "But I'm going to stop it."

Several bodies were littered about, a grieving Mr. Cake held poor little Pound Cake in his arms, not breathing

"This is terrible…" Luna said

"You see what a war brings" the Doctor said, "And your kind isn't ready for it."

Lyra choked back a sob, the Doctor simply looked over the maelstrom and took a breath

"What do we do Doctor?" Celestia asked

"Simple" the Doctor said, "Look for that taste in the air."

Lyra smacked her lips, "Yeah I think I can taste it."

"And that's where we're going?" Luna asked

"Right into the heart of this madness" the Doctor answered, "Try and talk about the good times you've had, Lyra and I have this."

Lyra took the Doctor's extended hand, together they walked off to the source of the strange taste…

Twilight had received news of the terrible explosion in Ponyville

"Applejack! I'm going to Ponyville!" Twilight called

Before her honest friend and companion could object she used her magical teleport and appeared on the dirt road leading into the forest

And the Doctor ran right into her

"Twilight?"

"Doctor!" Twilight gave the shocked Doctor a hug

"What are you doing here?" the Doctor asked

"I heard about the explosion, I figured I should help out." Twilight answered

"I'm off to stop this from going any further" the Doctor said, "I'd recommend you help them out back there, they'll need you."

The Doctor and Lyra continued their reckless sprint through the plains and over to the forest, the place of origin was a small little cottage

"Doesn't this place belong to Fluttershy?" Lyra asked

"If so then she's been out for a bit hasn't she?" the Doctor commented

The Doctor walked up to the door, he tried it and it was locked

"How are we getting in?" Lyra asked

"Like this" the Doctor used the sonic on the door and walked inside

The house was dark, but the Doctor could taste it by now, it was powerful, and he felt a deep movement inside himself

"What could be in here?" Lyra asked, "Fluttershy is harmless."

"She might be but whatever's down here is definitely not." The Doctor pulled a few floorboards up

"Ah and there it is!" the Doctor showed Lyra a small metal device

"What's that?" Lyra asked, feeling uneasy

"An emotion inhibiter" the Doctor answered, "Same tech in Cybermen but it seems this one had its polarity reversed."

"And that does?"

"It has a set emotion that it attempts to spread, in this case it has jealousy and anger." The Doctor said, "And nobody can find out exactly why they were so angry."

"Does this mean it's over?" Lyra looked at the inhibiter

"Not yet" the Doctor said, "Once I change this back there's going to be a flow of happy emotions, ready?"

"Always"

"Allonsironimogi!" the Doctor used the sonic on it

The device sparked and gave off a puff of smoke but otherwise did nothing

"Is that it?" Lyra asked

"It seems to be, but Equestria has some healing to do before anything." The Doctor smiled sadly, "Only if more had lived."

The Doctor stood up and walked out front of the cottage, several ponies were going around with broad smiles and giving out hugs

"Well Pinkie's going to have a field day" Lyra noted

"Well that's going to be interesting, she does so every day." The Doctor chuckled

"Require a lift Doctor?" Luna was nearby

"I think a walk would be nice, time to take in why I'm even here." The Doctor said

"Why are you here anyway?" Twilight asked

"When I first arrived, the Univore was why the walls were weak, but now that it's gone the walls are back, I'm trapped." The Doctor said

"What are you going to do now?" Celestia asked

"Travel through time and space as usual" the Doctor looked over to the park

A mare trotted by, "Wait, weren't you in the park with that box?"

"I was WHAT!" the Doctor ran towards the park

There he found the TARDIS in the middle of travel, it was leaving

The Doctor took out his sonic and used it on the TARDIS, it sparked and the sonic fell to the ground, smoking

"_In the skin of whom you trust most Doctor…_" the voice said before the TARDIS vanished completely


	8. Age of Steel

"Doctor?" Twilight caught up

"Someone took my TARDIS" the Doctor said, "Celestia do you happen to have anything that I can use?"

"I have some technology from when you first arrived but-"

"Show me" the Doctor ordered

"You might not be very-"

"I said show me" the Doctor repeated

Princess Celestia hailed her royal cab, in other words the chariot. I just like the idea of a royal cab

The Doctor was riding shotgun, Luna was giving Lyra the ride to Canterlot

"Now I must warn you, this technology has proven to be quite… picky." Celestia said

"If it's tech I can handle it." The Doctor stated

The chariots made haste, meanwhile the Doctor tried to figure out what exactly stole the TARDIS

It wasn't a pony, the mare said it looked just like him, so it was humanoid, and if it looked like him then that meant

"We have arrived" Celestia interrupted the Doctor's thoughts

"Alright" the Doctor hopped over the edge and landed

"Doctor, are you sure this is a good idea?" Lyra asked

"No idea" the Doctor said, "But without the TARDIS we may all be in grave danger."

"So we're taking a risk for a risk?" Luna summed up

"Yeah pretty much" the Doctor said, "As I said before, Allonsy."

Celestia showed the small group the entrance to the tower where the elements used to be kept

The door opened, and the Doctor felt his pulse quicken

"You were harboring Dalek technology?" the Doctor demanded, "If one piece was active you'd all be dust by now!"

"We were simply preparing." Celestia said

"Thankfully I can use this to get home" the Doctor said, "And find the TARDIS."

"How is this junk going to help?" Shining Armor appeared behind him

"I'll show you" the Doctor said, "Let's started."

The Doctor was going through the littered pieces of Daleks and Shining Armor was helping out however he could

"Can't this go any faster?" one of the guards asked

"Without my sonic this might take hours" the Doctor said, "Maybe even days."

"Well all the screwdriver does is use sonic resonance right?" Celestia asked, "We could find a unicorn that can do that."

"No" the Doctor said, "That would fry their horn even if they did it right."

"So it'll take a couple days?" Luna asked

"If I'm correct." The Doctor sighed, "Maybe if I power the time vortex through the- oh!"

The Doctor shot to his feet, "I've traveled through universes before! I can use the leftover energy to power the emergency temporal shifter!"

"The what?" Lyra asked

"It's something the daleks use to escape whenever they're in too grave danger." The Doctor explained, "And I can use that to track the TARDIS!"

The Doctor picked up several cables and a few things Lyra didn't know what were and started building something in the middle of the floor

"Is it dangerous?" Luna asked

"Daleks have a protective shell, but I don't. So I'll be in plenty of danger, but you'll be fine. I think." The Doctor said

The Doctor's watch beeped

"Is it really that time again?" the Doctor looked at it, "That means- wait a minute! I know exactly where I'd go if my watch went off!"

Shining Armor plugged in the plungers, "Where are you going?"

"I think I can land nearby the time the TARDIS will land" the Doctor said; messing with the wires, "I'll have to avoid causing a panic."

"Why would you cause a panic?" Lyra asked

"Well if he's convinced them he's me, then it'll be bad if they find me sneaking around." The Doctor explained

"When will I see you again?" Lyra asked

The Doctor paused, "I don't know, I think I'll see you again but I can't be sure."

"Well off you go then" Celestia said, "If we're in danger I'd leave it to the old and trusted Doctor."

"You seem to be respecting me more and more" the Doctor noted

"Don't get used to it" Luna winked

The Doctor smiled, "Then adventure awaits"

The Doctor pressed a few more buttons, he then powered it on

"Will you live?" Shining Armor asked

"One way to find out" the Doctor said, "Allonsironimogi!"

Then he grabbed the plungers

It was the year 1010 of Celestia's reign as ruler of Equestria, the Doctor landed in Canterlot in the throne room

"Ohh! Time travel without a capsule that's a killer!" the Doctor stretched, "I'll have to avoid swimming for a half hour."

The sound of ponies on the move got the Doctor hidden in the closest shadow; they were oblivious to the fact that he was hidden

"So you had regenerated again?" a voice asked, a younger version of Twilight

"Well with my luck and experiences" a voice said, "You learn to get used to it."

The Doctor held his breath, a man stepped into view

He wore a brown coat that went down to his waist; his hair was ginger and his eyes were a vibrant green

'Why does he get to be ginger?' the Doctor complained to himself

He also had a fedora; green pants and brown shoes

"If you say so Doctor" Twilight said as they continued towards the concert room

The Doctor looked around the corner, the group had moved on and the coast was clear

He continued, trying to figure out exactly what he was going to do when he realized he was at the doors

Vibrant party music was playing on the other side; the bright lights signaled what could only be a Pinkie Pie party

The Doctor shoved open the doors and strode in, a few ponies stopped to look at him

Then the whole party went silent

Not a single pony could think of what to say, until Rainbowdash happened

"Does anypony have an explanation for this?"

"I do" the Doctor said, "This man is celebrating my birthday party thinking he's me."

The man who claimed to be the Doctor strode up to him

"How are you here?"

"I followed you" the Doctor said, "I tend to do that when someone takes my TARDIS."

"You can't be here! Think of the paradoxes!" the man exclaimed

"How old are you turning?" the Doctor asked

"Oh! That means I can get the candles for the cake!" Pinkie Pie exclaimed

"1,224" the Doctors said at the same time

"That's not possible" the man said

"If we're the same age then you're not my future" the Doctor said, "You can't exist."

"Green shoes, what were you thinking?" the man changed the subject, pointing at the Doctor's shoes

"Better than green pants" the Doctor countered

"They're cool"

"Says someone who isn't supposed to exist" the Doctor crossed his arms, "And furthermore-"

The windows shattered, several Cybermen walked through

"Ohh! We were too busy arguing we didn't think to listen for threats!" the Doctor mentally kicked himself

"Talking's all well and good but we have civilians to save!" the 'Doctor' said

"What do we do Doctor?" Twilight asked

(For the sake of sanity, I'll call him John Smith because this is confusing)

"They won't go after you" Smith said

"They want humanoids" the Doctor finished, "They're after both of us."

"Delete" the Cybermen repeated

"Hey Cybermen!" the Doctor was by the DJ

"You are designated as the Doctor" one cyberman said

"With a community of intelligent ponies" the Doctor said, "Remember what happens with sound?"

"Wubs!" the DJ finished

She hit it; the sound waves were blasting through the crowd and causing all machines to malfunction

A few Cybermen grabbed their heads as their brains melted

"Let that be a lesson to you" the Doctor said as they Cybermen hit the ground

"What were they?" a mare asked, she was holding a bow from a cello

"Cybermen, they used to be human before their brains were removed and put into a metal shell" Smith said

"All emotions were restrained, they can't feel." The Doctor finished

"You two, you're perfect for each other." Twilight commented

The two timelords looked at each other

"After we settle this, we'll settle how you're real." The Doctor said

"Fine by me" Smith and the Doctor shook on it

The Doctor reached into his coat, "We can try and figure out where the leader is and stop him."

"First, we should find the signal." Smith said

The Doctor started to gather materials from the Cybermen, Twilight looked at them in worry

"What do they want?" Twilight asked

"To make every living thing like them" the Doctor said, "But ponies aren't compatible so they can't convert you."

"Alternatively they might use you for power, unicorn's magic and all." Smith finished

"Are we in danger?" a pony asked

"Almost certainly" the Doctor said, "Now then."

He held up a small device, pressing the button and it gave a small beep

"This will lead us directly to any non-terrestrial equipment, namely the Cybermen." The Doctor explained

The Doctor and Smith began to follow the machine, it showed them through the rack and ruin of the castle

"These Cybermen are certainly determined" Smith noted

"But why here? Ponies aren't compatible" the Doctor pointed out, "They have no reason to be here at all."

"Remember what unicorns are capable of?" Smith asked, "Their magic is power."

"That isn't it" the Doctor shook his head, "The Cybermen have all the power they need as for now."

Smith sighed, "I assume we lost the signal?"

"No, it's pointing…" the Doctor looked into the sky, "Right there, they have a ship."

"What kind?"

"CyberKing, dreadnaught class." The Doctor answered, "But that makes no sense! Why have a CyberKing above a planet that they can't convert!"

"Unless…" Smith paused

"No; they couldn't have had the dignity to adapt." The Doctor said

"I have a vortex manipulator, let's find out." Smith suggested

"I'm so going to regret this" the Doctor sighed, "But there isn't much we can do down here is there?"

Smith pressed a few buttons, the Doctor held on

And then they warped

MEANEWHILE

The lone stallion snuck around the massive ship in the sky, remaining unnoticed by the guards

'These are the ones who took her…' he thought darkly

He snuck around one of the passages, there was a door blocking his way

The Doctor and Smith arrived on the ship, several Cybermen were standing there

"Doctor"

"Yes well, hello there!" the Doctor said

"You have shown up at the precise time we calculated"

"We're going to stop this." Smith proclaimed

"Incorrect, for we have a secret weapon."

"Oh is that so?" the Doctor said, "You know, a planet of those you can't convert isn't very use-"

A four legged metal pony stepped out of the shadows

"Behold, the Cyberman Mk II"

"You had to bring it up didn't you?" Smith asked

"So you have Cyberponies" the Doctor shrugged, "But does it really matter? We're going to stop you anyway."

In truth the Doctor's heart was pounding, if they could convert ponies then they could have an army within moments with the CyberKing

"I hope you have a plan" Smith said as the Cybermen drew closer

"You know what my plan is with this" the Doctor rolled his eyes, "Run!"

The Doctor and Smith bolted, running down the corridor and avoiding laser blasts

"This is your plan!?"

"1,224 years of running! And it hasn't failed me yet!" the Doctor answered

The pair reached a giant metal door, Smith tossed the Doctor his sonic screwdriver

"Get that door open" Smith ordered, "I'll distract them!"

"I'm not even going to ask how" the Doctor got to work on the door

Smith checked to see that the Doctor wasn't watching, then he extended his right arm forward, a metal blaster came out of his wrist

"You have been identified as rouge elements" the Cyberpony said, "You will be deleted"

Smith fired, the Cybermen fired back

The Cybermen had much better aim than Smith did, it was a lucky shot that had nailed him in the shoulder

Smith collapsed, the Doctor turned and tried to keep him awake

"I know who I am now" Smith smiled, "I'm just another soul who tried to save you."

"Come on!" the Doctor said, "You can pull out of this!"

Smith stood up, "Keep the sonic, and take this."

Smith handed the Doctor his fedora

"What about you?" the Doctor asked

"Like I said" Smith extended the blaster again, "I'm a Cyberman, one who feels."

The door opened behind the stunned Doctor

"Doctor?" a voice asked

The Doctor turned around, "Clock Crasher?"

Clock Crasher grabbed the Doctor and threw him behind the door, locking the pair inside

On the other side of the door they could hear Smith's last cries of pain


	9. Age of Steel 2

"Who was that with you?" Clock Crasher asked

"A robot doppelganger of me, one who fought the Cybermen." The Doctor speculated, "Must have used an actual mind, thus giving him will."

"But never mind that" the Doctor said, "What are you doing up here?"

"They captured Starlight" Clock Crasher answered, "I was hoping I could get here in time."

The dark expression on the Doctor's face said it all

"They got her didn't they?" Clock Crasher slumped, "I couldn't protect her, I'm sorry."

"Not your fault" the Doctor put on the fedora, "For now, you're coming with me."

Clock Crasher stood up, "So where to then?"

"We should get back to the TARDIS, I have an idea." The Doctor answered

Clock Crasher followed the Doctor through the corridors

They soon found an intersection, Cybermen stomped through from each side

"What now Doctor?" Clock Crasher asked

"Don't worry, I have a plan."

* * *

The bedraggled looking pair stepped up to the TARDIS

"That plan was insane" Clock Crasher commented

"We survived didn't we?" the Doctor countered, "Now we can find out exactly where these Cybermen are."

The Doctor tried the door, it didn't budge

Confused he put the key in the lock, the Cloister Bell went off

"The TARDIS must be repairing from the crash." Clock Crasher said

"Right no TARDIS and no other ideas" the Doctor scratched the back of his head, "I'm open to suggestions."

"Let's talk to the princess" Clock Crasher said, "She's bound to have seen something."

So together the pair went to the castle, unaware of the silver rat in the shadows behind them

Twilight was with her friends in the room where the party was interrupted

"So we're supposed to sit back while he goes and fights robots?" Rainbowdash asked

"You saw what happened" Twilight said, "We can't touch those things."

"They ruined a perfectly good party too." Pinkie Pie added

"Well if I see them around I'll show them not to attack my friends!" Rainbowdash made punching motions

"Until I say so" the Doctor walked in, "Nobody is going near a Cyberman."

"What?" Applejack asked, "Why not?"

"They've improved technology" the Doctor answered, "Now you're all at risk for conversion."

"So what do you suggest we do?" Celestia asked

"I simply came here for a plan" the Doctor answered, "My TARDIS is damaged so I can't use that."

"Wait, where's John Smith?" Twilight asked; noticing the Doctor had his fedora

"He's gone" the Doctor answered simply, "He did it to save my life."

"Why didn't you try to save him?" Rainbowdash demanded

"I thought I wasn't alone anymore" the Doctor sighed, "It turned out he was as machine as the Cybermen."

A short silence filled the room

"So what do we do?" Luna asked

"The Cybermen have a massive ship up above" Clock Crasher said

"One able to convert millions in minutes." The Doctor finished

There was an even longer silence, this one filled with shock

"M-millions?" a mare stuttered, she fainted and dropped her Cello bow

"That's more than Equestria happens to have." Celestia mentioned

"So they can convert all of Equestria in minutes" the Doctor said

"A giant CyberKing in orbit around a planet this size I'd say it gets here in say… Twenty minutes?"

"Right" the Doctor agreed, "Twenty minutes and I have no TARDIS and a backup sonic screwdriver."

"You also have us!" Rainbowdash saluted

"Put your hoof down, I don't do salutes." The Doctor waved his hand

"How can we help?" Twilight asked

"Those machines are simply dreadful" Rarity said, "They need a new color."

"Or they need to be blasted out of the sky." The Doctor said

"But the elements are in Ponyville, it'd take us a half hour to get there at best." Twilight pointed out

"Not a problem, not one at all!" the Doctor reached into his coat pocket and pulled out a leather device

"Where'd you get that?" Clock Crasher asked

"Duh" Pinkie Pie said, "The author had to make it possible that we'd get there; so he had Smith give it to him off screen!"

The whole group dismissed that as Pinkie just being Pinkie

"So we're going to go to Ponyville?" Twilight asked, "I doubt that thing's bigger on the inside."

"It's just cheap time travel" the Doctor answered, "Put your hoof on it and I can bring us to Ponyville from here."

The mane six and the two versions of the Doctor got ready

The Doctor hit it

* * *

The small band appeared in Ponyville; with aching muscles and joints

"Time travel without a capsule" the Doctor said, "That one's a killer!"

"Where are we?" Rainbowdash asked

"We're right by Sugarcube Corner" Pinkie Pie bounced

"No time to dawdle about this time!" the Doctor jumped to his feet, "We've got a planet to save!"

The group rushed to the library, the residents of Ponyville unaware of the danger that was coming to bear upon the small town

"Are we even sure the elements are going to do it?" Clock Crasher asked

"No idea" the Doctor answered, "Then again, do you have a better plan?"

Clock Crasher shook his head

Twilight used her magic to float the elements over to her friends

"They'll have to be in range of the ship" the Doctor said

"What's the range of the elements anyway?" Clock Crasher asked

There was a group of murmurs, they had no idea

"Fantastic" the Doctor sighed, "We'll have to keep the Cybermen busy until you can get in range."

"We'll do what we can for now." Twilight aid

"Clock Crasher, with me." The Doctor said, "I'm thinking of the perfect distraction…"

The Doctor and Clock Crasher rushed out of the library, Clock Crasher looked at the Doctor. Expecting to hear the plan

"Right, I'll need to find something big" the Doctor said, "Something that's big and pointy, something like a tower of some sort…"

Clock Crasher made a gesture behind the Doctor

The Doctor turned around, seeing the castle

"What?" he asked

Clock Crasher pointed at the tower that Luna lived in

"Oh now I get it." The Doctor said; then he looked at his watch

11 minutes

"Right, we've got to get to that tower and I know exactly how to get there!"

The seven ponies and one timelord were at the tower, the hot air balloon they used was crashed over the Canterlot Park

"Did you really have to hook up the vortex manipulator to the hot air balloon?" Rainbowdash asked

"No" the Doctor said, "But it was fun!"

"What exactly do you plan on using my tower for?" Luna asked, landing next to them

"Simple, we use it as a-" the Doctor's watch beeped, "And the ship should be coming into the atmosphere about now."

Right on cue the giant CyberKing broke through the cloud layer; the Doctor grabbed a microphone from the DJ booth

"This is your one warning" the Doctor said, "Leave this planet and never return, otherwise drastic measures will be taken."

The Cybermen answered back

"We are uniform, we are the Cybermen. And soon so shall be these equines."

"That was your one warning" the Doctor shrugged, "Hit it Twilight."

…

The elements remained silent

"Twilight?" Clock Crasher asked

"We have disabled all elemental magic in this land" the Cybermen reported, "This plan was futile, now this world will be deleted."

The Doctor grabbed Clock Crasher and hit the vortex manipulator

They appeared on the CyberKing, the duo were down in the boiler room

"What's your plan now?" Clock Crasher asked

"If we can't use harmony, let's use our own wit." The Doctor said, "No time to explain!"

The Doctor ran down to a few of the machines, pressing all the random buttons he could; Clock Crasher did the same

Red sirens were going off and several Cybermen burst into the room, surrounding the two

"You have been designated as rouge elements, you will be deleted."

"Well I'd love to" the Doctor said, "But I really have somewhere to be."

The Doctor and Clock Crasher used the vortex manipulator to get back down to the castle

The ship was retreating back into space, in order to get the giant laser ready

The boiler room overheated and blew, causing a chain reaction that blew out the core, effectively blowing up the ship

Twilight and her friends watched as the ship began to swell, then they saw the whole ship blow

"Where's the Doctor?" Fluttershy asked

"How dreadful!" Rarity exclaimed, "He was on board!"

"He'll be remembered" Luna said

The Doctor then appeared in the middle of the group

"Huh, not dead." The Doctor smiled, "Nice thought."

"You've saved Equestria once again" Luna smiled, "You are truly a hero."

"Oh stop it" the Doctor said, "Anyone can save the planet if they know how, look at the six around you. They've done it before."

*DONG*

The Doctor reached into his coat pocket, pulling out his key. It showed that the TARDIS was done repairing

"Ah, yes; well." The Doctor said, "I believe it's my cue to be off."

"What about those ruffians; the Cybermen?" Rarity asked

"They'll be gone" the Doctor said, "That ship had a reactive core."

"So you killed them?"

There was a silence

"There was no other choice." The Doctor said

Then he went back to the TARDIS

"Alright, what do you have for me this time?" the Doctor swung the doors inward, "New look, let's take a closer one shall we?"

The console was circular, a metal grate floor above the circuitry and a tall glass funnel leading up to the ceiling, a long clear cylinder floated in the center. The familiar shapes on the walls were once again circles and the overall desktop color was a light blue

"Well, certainly is a nice look." The Doctor smiled, then he smiled and entered

Clock Crasher opened the doors, "You're not leaving on your own are you?"

"Well I was planning on picking someone up, you want to come?" the Doctor asked

Clock Crasher nodded, "It's better than staying here."

The Doctor put in the time and the place on the console, it wasn't a cluttered as it was before. The chameleon circuit read as out of order, there was a keyboard and the monitor was an old computer screen. The Doctor ran around the machine, punching buttons and flipping switches, then he grabbed the handbrake, which looked like a parking brake.

"Well then." The Doctor smiled, "New TARDIS, new hat and a new companion. Allonsironimogi!"


	10. Setup

A/N: This chapter was shortened exponentially as it is just a set up for later 'episodes', sorry for any inconvenience

Rainbowdash opened the TARDIS door, "Hey, where do you think you're going?"

"Well" the Doctor said, "Back to the TARDIS, same old life."

"You skipped out on your last party" Rainbowdash shook her head, "You're not skipping out this time."

"I don't think sticking around is a good idea" Clock Crasher said, "But Pinkie may want you to be there."

The Doctor sighed, "Fine, I'll be there for this one time."

"SURPRISE!" a large group of ponies jumped out from various areas

After the Doctor was sure he wouldn't have a stroke anytime soon he asked the major question

"How did you get in here?"

"That'd spoil the surprise" Pinkie Pie said, "Duh!"

"I just got in here-" the Doctor sighed, "Never mind."

"Woo! Nice time machine!" Pinkie Pie said

"Nobody touch the controls!" Clock Crasher warned, "You might fly us into a supernova!"

"Seems rather dangerous, don't you agree Doctor?" Luna asked

"It's only meant for those who know how to fly it." The Doctor answered

"It _is_ bigger on the inside." Celestia commented, walking up to the Doctor. "Why a phonebox?"

"What?"

"It's a police phone box, why's that?" Twilight clarified

"Well the TARDIS has this thing called the chameleon circuit" Clock Crasher started, "When it first lands in a new place it scans everything within a 100 mile radius of it and decides what would best fit in."

"Then it disguises itself as a police telephone box from 1963" the Doctor finished, "It broke a while ago, but I liked the look so I never got around to fixing it."

"So you travel through time and space in a wooden box that's bigger on the inside?" Applejack summed up

"And have adventures all the way." The Doctor said

"Awesome!" Rainbowdash exclaimed, "Can I come?"

"No." the Doctor asserted, "Nobody can come with me."

"Why not?" Rainbowdash moaned

"I've had companions before" the Doctor said, "And I've lost them, lost them all."

"What of your home planet?" Luna asked, "And the timelords?"

"You did say you were the last of the timelords." Twilight noted

"Alright" the Doctor said, "I'll tell you, but someone please cover Fluttershy's ears."

(Cue epic flashback)

"Gallifrey was a beautiful planet, it used to be called the shining world of the seventh system. And on the continent of Wild Endeavor, nestled upon the never ending mountains of Solace and Solitude, there was the Citadel of the Timelords." The Doctor explained, "The oldest and mightiest race in the universe, now what my people did was they went to war, a time war. The last great time war."

"War with whom may I ask?" Luna asked

"The timelords went to war with a race of beings called the Daleks." Clock Crasher said, "The daleks wanted one thing: To exterminate all beings that weren't dalek. The timelords fought them for all creation."

"The timelords died but took the daleks with them" the Doctor finished, "Don't make me go into detail how."

The TARDIS monitor lit up, it showed a picture of a dalek

"That's a dalek, you remember them." The Doctor said, "They are my worst enemies."

"Then why did you let them go?" Rainbowdash asked

"I had more pressing matters." The Doctor answered, "Like surviving the Princess's attempts to 'eliminate the human'." The Doctor laughed

Celestia gave him a look

The Doctor shrugged

"Is this a party or an interrogation?" Clock Crasher asked

The rest of the night went by without incident, the Doctor stayed away from the alcoholic drinks, he remembered the last time

The last ponies to go were going to be Applejack and Twilight

"See you later Doctor" Twilight said as she was at the door, "Good luck."

"Have fun Doc" Applejack tipped her hat

The Doctor waved

The Doctor stepped up to the console, it was spacious and clean, the controls were slightly less random than his last few versions

"Where to Doctor?" Clock Crasher asked

"In the TARDIS?" the Doctor smiled, "Next stop: Everywhere."

The Doctor reached to touch the controls, but the TARDIS lurched and threw the timelord to the side

"What!" the Doctor exclaimed in shock

The Doctor grabbed one of the many floating pillars in the control room, it held firm

"Doctor! What did you do!" Clock Crasher asked

"I didn't do anything!" the Doctor called back, "The TARDIS is flying itself!"

NEXT TIME:

"The TARDIS is sick" the Doctor was checking the core

"Rainbowdash! How did you get here?"

A sound was heard in the shadows of the control room, and then it lunged


End file.
